University of Oulu

Kvist, L., Niskanen, M., Mannermaa, K., Wutke, S., & Aspi, J. (2019). Genetic variability and history of a native Finnish horse breed. Genetics Selection Evolution, 51(1).

Genetic variability and history of a native Finnish horse breed

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Author: Kvist, Laura1; Niskanen, Markku2; Mannermaa, Kristiina3;
Organizations: 1Department of Ecology and Genetics, University of Oulu, POB 8000, 90014 Oulu, Finland
2Research Unit of History, Culture and Communications, University of Oulu, POB 8000, 90014 Oulu, Finland
3Department of Philosophy, History, Culture and Art Studies, University of Helsinki, POB 24, 00014 Helsinki, Finland
4Department of Environmental and Biological Sciences, University of Eastern Finland, POB 111, 80101 Joensuu, Finland
Format: article
Version: published version
Access: open
Online Access: PDF Full Text (PDF, 2.5 MB)
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Language: English
Published: Springer Nature, 2019
Publish Date: 2019-09-04


Background: The Finnhorse was established as a breed more than 110 years ago by combining local Finnish landraces. Since its foundation, the breed has experienced both strong directional selection, especially for size and colour, and severe population bottlenecks that are connected with its initial foundation and subsequent changes in agricultural and forestry practices. Here, we used sequences of the mitochondrial control region and genomic single nucleotide polymorphisms (SNPs) to estimate the genetic diversity and differentiation of the four Finnhorse breeding sections: trotters, pony-sized horses, draught horses and riding horses. Furthermore, we estimated inbreeding and effective population sizes over time to infer the history of this breed.

Results: We found a high level of mitochondrial genetic variation and identified 16 of the 18 haplogroups described in present-day horses. Interestingly, one of these detected haplogroups was previously reported only in the Przewalski’s horse. Female effective population sizes were in the thousands, but declines were evident at the times when the breed and its breeding sections were founded. By contrast, nuclear variation and effective population sizes were small (approximately 50). Nevertheless, inbreeding in Finnhorses was lower than in many other horse breeds. Based on nuclear SNP data, genetic differentiation among the four breeding sections was strongest between the draught horses and the three other sections (FST=0.007–0.018), whereas based on mitochondrial DNA data, it was strongest between the trotters and the pony-sized and riding horses (ΦST=0.054–0.068).

Conclusions: The existence of a Przewalski’s horse haplogroup in the Finnhorse provides new insights into the domestication of the horse, and this finding supports previous suggestions of a close relationship between the Finnhorse and eastern primitive breeds. The high level of mitochondrial DNA variation in the Finnhorse supports its domestication from a large number of mares but also reflects that its founding depended on many local landraces. Although inbreeding in Finnhorses was lower than in many other horse breeds, the small nuclear effective population sizes of each of its breeding sections can be considered as a warning sign, which warrants changes in breeding practices.

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Series: Genetics selection evolution
ISSN: 0999-193X
ISSN-E: 1297-9686
ISSN-L: 0999-193X
Volume: 51
Article number: 35
DOI: 10.1186/s12711-019-0480-8
Type of Publication: A1 Journal article – refereed
Field of Science: 1181 Ecology, evolutionary biology
1184 Genetics, developmental biology, physiology
Funding: This research was funded by the Finnish Cultural Foundation and the University of Oulu.
Copyright information: © The Author(s) 2019. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (, which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( applies to the data made available in this article, unless otherwise stated.